Wikiomics:DNA sequencing: Difference between revisions
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* [http://www.454.com/enabling-technology/the-software.asp Newbler Assembler] software from 454 for de novo sequence assembly. | * [http://www.454.com/enabling-technology/the-software.asp Newbler Assembler] software from 454 for de novo sequence assembly. | ||
====Experimental==== | |||
* [http://sharcgs.molgen.mpg.de/index.shtml SHARCGS], a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage. | |||
* [http://www.genome.org/cgi/content/full/18/5/810 ALLPATHS (HTML)] algorithm only | |||
* [http://maq.sourceforge.net/maq-man.shtml Maq] mapping short reads to an existing genomic sequence | |||
See also software from | See also software from | ||
* [http://www.bcgsc.ca/platform/bioinfo/software/ GSC Software Centre] at Canada's Michael Smith Genome Sciences Centre. | * [http://www.bcgsc.ca/platform/bioinfo/software/ GSC Software Centre] at Canada's Michael Smith Genome Sciences Centre. | ||
===Sequence databases & formats=== | |||
* [http://srf.sourceforge.net/ SRF] a generic format for DNA sequence data | |||
* [http://www.ncbi.nlm.nih.gov/Traces/sra/ The Short Read Archive @NCBI] | |||
===Short reads assembly (Solexa etc)=== | ===Short reads assembly (Solexa etc)=== |
Revision as of 11:16, 30 July 2008
Base calling (ABI)
- phred giving more accurate calls for less accurate part of the sequence (like at the end of the run, say 600bp and more) . Phred also gives a probability/quality values for each of the bases allowing more accurate assembly. Quality scores range from 4 to about 60, the "high quality bases" are these with scores > 20.
- To run it you need to set up PHRED_PARAMETER_FILE variable.
Bash shell:
export PHRED_PARAMETER_FILE=/path/to/your/file/phredpar.dat
- To see all the options:
phred -doc | less
- To do simple basecalling on _all_ files in a input_directory and store the SCF files in scf_output_directory:
phred -id input_directory -cd scf_output_directory:
Caveat: names of the new SCF files will be the same as input files.
- LifeTrace from Incyte. Usage info from U.Bielefeld. Comparable with phred, better than phred on MegaBACE sequences. Not available from original Incyte web site (080624).
- Long Trace & Peak Trace from Nucleics. Claims to increase the lenght of readable bases by ca 80bp. Separate software module for increasing daily throughput of a capillary sequencer.
Sequence assembly
See and read!: http://www.cbcb.umd.edu/software/
First generation
Genome assemblers used in current genomic projects
- JAZZ -> @JGI in house only
- RAMEN (not published yet as for 08-6-17), used for medaka and silkworm genome sequencing projects
New Programs
- MIRA latest version 2.9.25 enables true hybrid sequence assembly (454 data [GS20 or GS FLX], Solexa with Sanger reads).
- SSAKE program for assembly milions of short sequences
- Newbler Assembler software from 454 for de novo sequence assembly.
Experimental
- SHARCGS, a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage.
- ALLPATHS (HTML) algorithm only
- Maq mapping short reads to an existing genomic sequence
See also software from
- GSC Software Centre at Canada's Michael Smith Genome Sciences Centre.
Sequence databases & formats
- SRF a generic format for DNA sequence data
- The Short Read Archive @NCBI
Short reads assembly (Solexa etc)
- Velvet Paper(HTML) De Bruijn Graphs based asembler from EBI (Zerbin & Birney)
Contig ordering/finishing
- Hawkeye interactive visual analytics tool for genome assemblies